I would take smaller squads of IST's, with 2 MG's, and put 'em in a rhino. if you don't take smaller squads...you may as well take sisters! Theme or no theme, 1 point for better armor and guns is amazing. IST's are all about taking advantage of that high special weapon/troop count ratio, IMHO.

Anywho...looks like a lot of fun! You'll just have to be really careful about clearing undesirable opponents away from your Engines and Flagellants, so that they don't get locked up in a horde of minis, or, particularly for your Engines, caught with a higher initiative, high str opponent.